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The molecular basis for flexibility in the flexible filamentous plant viruses


Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity.

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Figure 1: The BaMV helical capsid structure.
Figure 2: BaMV cryo-EM reconstruction allows building and refinement of atomic models.
Figure 3: The refined model reveals atomic details.

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  1. Kendall, A. et al. J. Virol. 82, 9546–9554 (2008).

    Article  CAS  Google Scholar 

  2. López-Moya, J. & García, J. in Encyclopedia of Virology Vol. 3, 1369–1375 (Academic Press, 1999).

  3. Chen, T.H. et al. Virus Res. 166, 109–115 (2012).

    Article  CAS  Google Scholar 

  4. Yang, C.D. et al. BMC Biotechnol. 7, 62 (2007).

    Article  Google Scholar 

  5. Shukla, S. et al. Nanomedicine (Lond) 9, 221–235 (2014).

    Article  CAS  Google Scholar 

  6. Zhang, T. et al. PLoS Biol. 4, e3 (2006).

    Article  Google Scholar 

  7. Lico, C., Chen, Q. & Santi, L. J. Cell. Physiol. 216, 366–377 (2008).

    Article  CAS  Google Scholar 

  8. Bernal, J.D. & Fankuchen, I. J. Gen. Physiol. 25, 147–165 (1941).

    Article  CAS  Google Scholar 

  9. Beijerinck, M.W. Versl. Gew. Verg. Wis en Natuurk. Afd. 7, 229–235 (1898).

    Google Scholar 

  10. Namba, K. & Stubbs, G. Science 231, 1401–1406 (1986).

    Article  CAS  Google Scholar 

  11. Ge, P. & Zhou, Z.H. Proc. Natl. Acad. Sci. USA 108, 9637–9642 (2011).

    Article  CAS  Google Scholar 

  12. Richardson, J.F., Tollin, P. & Bancroft, J.B. Virology 112, 34–39 (1981).

    Article  CAS  Google Scholar 

  13. Kendall, A. et al. Virology 436, 173–178 (2013).

    Article  CAS  Google Scholar 

  14. Yang, S. et al. J. Mol. Biol. 422, 263–273 (2012).

    Article  CAS  Google Scholar 

  15. Lin, N.S. et al. J. Gen. Virol. 75, 2513–2518 (1994).

    Article  CAS  Google Scholar 

  16. Lin, M., Kitajima, E., Cupertino, F. & Costa, C. Phytopathology 67, 1439–1443 (1977).

    Article  Google Scholar 

  17. Lan, P., Yeh, W.B., Tsai, C.W. & Lin, N.S. Mol. Plant Microbe Interact. 23, 903–914 (2010).

    Article  CAS  Google Scholar 

  18. Egelman, E.H. eLife 3, e04969 (2014).

    Article  Google Scholar 

  19. Leaver–Fay, A. et al. Methods Enzymol. 523, 109–143 (2013).

    Article  Google Scholar 

  20. Hung, C.J. et al. Mol. Plant Pathol. 15, 196–210 (2014).

    Article  CAS  Google Scholar 

  21. Chen, H.C. et al. Nucleic Acids Res. 40, 4641–4652 (2012).

    Article  CAS  Google Scholar 

  22. Lin, N.-S. & Chen, C.-C. Phytopathology 81, 1551–1555 (1991).

    Article  Google Scholar 

  23. Mindell, J.A. & Grigorieff, N. J. Struct. Biol. 142, 334–347 (2003).

    Article  Google Scholar 

  24. Frank, J. et al. J. Struct. Biol. 116, 190–199 (1996).

    Article  CAS  Google Scholar 

  25. Tang, G. et al. J. Struct. Biol. 157, 38–46 (2007).

    Article  CAS  Google Scholar 

  26. Egelman, E.H. Ultramicroscopy 85, 225–234 (2000).

    Article  CAS  Google Scholar 

  27. Rosenthal, P.B. & Henderson, R. J. Mol. Biol. 333, 721–745 (2003).

    Article  CAS  Google Scholar 

  28. Song, Y. et al. Structure 21, 1735–1742 (2013).

    Article  CAS  Google Scholar 

  29. DiMaio, F., Leaver–Fay, A., Bradley, P., Baker, D. & Andre, I. PLoS ONE 6, e20450 (2011).

    Article  CAS  Google Scholar 

  30. DiMaio, F. et al. Nat. Methods 12, 361–365 (2015).

    Article  CAS  Google Scholar 

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This work was supported by funds from US National Institutes of Health (NIH) GM035269, S10-RR025067 and S10-OD018149 (to E.H.E.); NSC98-2321-B-005-005-MY3 (to Y.-H.H.); NSC99-2628-B-001-012-MY3 and Academia Sinica (to N.-S.L.); and Scholarships for Excellent Students to Study Abroad from National Chung-Hsing University (to C.-C.C.). We thank K. Dryden for assistance with the cryo-EM. The cryo-EM work was conducted at the Molecular Electron Microscopy Core facility at the University of Virginia, which is supported by the School of Medicine and was built with NIH grant G20-RR31199. C.-C.C. thanks R.H. Cheng, L. Xing, R. Diaz, Z.H. Zhou and G.G. Liou for their assistance.

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Authors and Affiliations



C.-C.C. prepared the viral samples and did preliminary EM studies; Y.-H.H. and N.-S.L. initiated the studies, designed the viral constructs and provided guidance in the viral preparation; X.Y. did the EM and filament selection; E.H.E. did the image analysis and three-dimensional reconstruction; F.D. and B.F. did the molecular modeling; F.D. and E.H.E. wrote the paper; and all authors edited the manuscript.

Corresponding authors

Correspondence to Yau-Heiu Hsu, Na-Sheng Lin or Edward H Egelman.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Power spectrum from BaMV segments.

A power spectrum generated from the 97,767 segments used in the final reconstruction (wt and Nd35 combined). The yellow arrow indicates the layer line (at 1/35.2 Å-1) arising from the left-handed one-start helix, while the red arrow indicates the fourth order of this one-start helical layer line at 1/8.8 Å-1. The log of the intensities is shown to allow for the large dynamic range.

Supplementary Figure 2 Map-map and model-map agreement.

(a) The FSC between the wildtype and Nd35 maps shows an apparent resolution of ~5.6 Å. (b) Models were fit to the wildtype maps (“training”) and evaluated against the Nd35 map (“testing”). The models show good agreement to both, with an FSC=0.5 crossing of about 5.0 Å, and with minimal overfitting (compare training map agreement to testing).

Supplementary Figure 3 Alternate views of the assembly, showing each subunit colored separately to better illustrate the intricate subunit interactions.

(a, b) Axial views of the assembly, looking from the top (a) and bottom (b) along the helical axis (referring to top and bottom from Figure 2). (c) The same view as in Figure 2c.

Supplementary Figure 4 Structure building and refinement are well converged.

(a) The best-scoring C-terminal models sampled by our backbone extension method show good convergence, with only small backbone deviations. (b,c) After all-atom refinement in the context of the full capsid, the best-scoring 5 models show minimal diversity in the core, with most of the diversity coming in the surface loops on the outside of the capsid (b), and the C-terminus on the inside of the capsid (c).

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 (PDF 641 kb)

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DiMaio, F., Chen, CC., Yu, X. et al. The molecular basis for flexibility in the flexible filamentous plant viruses. Nat Struct Mol Biol 22, 642–644 (2015).

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